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At least 1,369 records · Page 76

Lipkin model on a quantum computer

Atomic nuclei are important laboratories for exploring and testing new insights into the universe, such as experiments to directly detect dark matter or explore properties of neutrinos. The targets of interest are often heavy, complex nuclei that challenge our ability to reliably model them (as well as quantify the uncertainty of those models) with classical computers. Hence there is great interest in applying quantum computation to nuclear structure for these applications. As an early step in this direction, especially with regards to the uncertainties in the relevant quantum calculations, we develop circuits to implement variational quantum eigensolver (VQE) algorithms for the Lipkin-Meshkov-Glick model, which is often used in the nuclear physics community as a testbed for many-body methods. Here, we present quantum circuits for VQE for two and three particles and discuss the construction of circuits for more particles. Implementing the VQE for a two-particle system on the IBM Quantum Experience, we identify initialization and two-qubit gates as the largest sources of error. We find that error mitigation procedures reduce the errors in the results significantly, but additional quantum hardware improvements are needed for quantum calculations to be sufficiently accurate to be competitive with the best current classical methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Iterative Learning Control for Video-rate Atomic Force Microscopy

We present a control scheme for video-rate atomic force microscopy with rosette pattern. The controller structure involves a feedback internal-model-based controller and a feedforward iterative learning controller. The iterative learning controller is designed to improve tracking performance of the feedback-controlled scanner by rejecting the repetitive disturbances arising from the system nonlinearities. We investigate the performance of two inversion techniques for constructing the learning filter. We conduct tracking experiments using a two-degree-of-freedom microelectromechanical system (MEMS) nanopositioner at frame rates ranging from 5 to 20 frames per second. Furthermore, the results reveal that the algorithm converges rapidly and the iterative learning controller significantly reduces both the transient and steady-state tracking errors. We acquire and report a series of high-resolution time-lapsed video-rate AFM images with the rosette pattern.

42 ENGINEERING↗

De novo Nanopore read quality improvement using deep learning

BACKGROUND: Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS: Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. CONCLUSIONS: MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub .

59 BASIC BIOLOGICAL SCIENCES↗

The GGCMI Phase 2 emulators: global gridded crop model responses to changes in CO 2 , temperature, water, and nitrogen (version 1.0)

Statistical emulation allows combining advantageous features of statistical and process-based crop models for understanding the effects of future climate changes on crop yields. We describe here the development of emulators for nine process-based crop models and five crops using output from the Global Gridded Model Intercomparison Project (GGCMI) Phase 2. The GGCMI Phase 2 experiment is designed with the explicit goal of producing a structured training dataset for emulator development that samples across four dimensions relevant to crop yields: atmospheric carbon dioxide (CO2) concentrations, temperature, water supply, and nitrogen inputs (CTWN). Simulations are run under two different adaptation assumptions: that growing seasons shorten in warmer climates, and that cultivar choice allows growing seasons to remain fixed. The dataset allows emulating the climatological-mean yield response of all models with a simple polynomial in mean growing-season values. Climatological-mean yields are a central metric in climate change impact analysis; we show here that they can be captured without relying on interannual variations. In general, emulation errors are negligible relative to differences across crop models or even across climate model scenarios; errors become significant only in some marginal lands where crops are not currently grown. We demonstrate that the resulting GGCMI emulators can reproduce yields under realistic future climate simulations, even though the GGCMI Phase 2 dataset is constructed with uniform CTWN offsets, suggesting that the effects of changes in temperature and precipitation distributions are small relative to those of changing means. The resulting emulators therefore capture relevant crop model responses in a lightweight, computationally tractable form, providing a tool that can facilitate model comparison, diagnosis of interacting factors affecting yields, and integrated assessment of climate impacts.

54 ENVIRONMENTAL SCIENCES↗

Solar structure inversion with LOWL data

Inversion results for the radial hydrostatic structure of the Sun, using six months of oscillation data obtained with the LOWL instrument, are presented. Both low and intermediate degree modes are used, thus avoiding the systematic errors that might have occurred in previous inversions by merging more than one data set. Using modes of between 0 deg and 90 deg and frequencies of between 1.5 mHz and 3.5 mHz, the variations with depth of the speed of sound, the density and the pressure were inferred for radii of between 0.05 and 0.85 stellar radius. It was found that in this region, the sound speed was within 0.15% of that of a model constructed using an equation of state that incorporated helium diffusion. The density difference between the Sun and the model was less than 0.8%. Given the small error bars on the inversion results, these differences are considered as being significant.

Basu, Sarbani↗

Columnar Aerosol Single-Scattering Albedo and Phase Function Retrieved from Sky Radiance Over the Ocean: Measurements of African Dust

The single-scattering albedo and phase function of African mineral dust are retrieved from ground-based measurements of sky radiance collected in the Florida Keys. The retrieval algorithm employs the radiative transfer equation to solve by iteration for these two properties which best reproduce the observed sky radiance using an assumed aerosol vertical structure and measured aerosol optical depth. Thus, no assumptions regarding particle size, shape, or composition are required. The single-scattering albedo, presented at fourteen wavelengths between 380 and 870 nm, displays a spectral shape expected of iron-bearing minerals but is much higher than current dust models allow. This indicates the absorption of light by mineral dust is significantly overestimated in climate studies. Uncertainty in the retrieved albedo is less than 0.02 due to the small uncertainty in the solar-reflectance-based calibration (12.2%) method employed. The phase function retrieved at 860 nm is very robust under simulations of expected experimental errors, indicating retrieved phase functions at this wavelength may be confidently used to describe aerosol scattering characteristics. The phase function retrieved at 443 nm is very sensitive to expected experimental errors and should not be used to describe aerosol scattering. Radiative forcing by aerosol is the greatest source of uncertainty in current climate models. These results will help reduce uncertainty in the absorption of light by mineral dust. Assessment of the radiative impact of aerosol species is a key component to NASA's Earth System Enterprise.

Cattrall, Christopher↗

A Physical Validation Program for the GPM Mission

The GPM mission is currently planned for start in the late 2007 - early 2008 time frame. Its main scientific goal is to help answer pressing scientific problems arising within the context of global and regional water cycling. These problems cut across a hierarchy of scales and include climate-water cycle interactions, techniques for improving weather and climate predictions, and better methods for combining observed precipitation with hydrometeorological prediction models for applications to hazardous flood-producing storms, seasonal flood draught conditions, and fresh water resource assessments. The GPM mission will expand the scope of precipitation measurement through the use of a constellation of some 9 satellites, one of which will be an advanced TRMM-like core satellite carrying a dual-frequency Ku-Ka band precipitation radar and an advanced, multifrequency passive microwave radiometer with vertical-horizontal polarization discrimination. The other constellation members will include new dedicated satellites and co-existing operational/research satellites carrying similar (but not identical) passive microwave radiometers. The goal of the constellation is to achieve approximately 3-hour sampling at any spot on the globe -- continuously. The constellation's orbit architecture will consist of a mix of sun-synchronous and non-sun-synchronous satellites with the core satellite providing measurements of cloud-precipitation microphysical processes plus calibration-quality rainrate retrievals to be used with the other retrieval information to ensure bias-free constellation coverage. A major requirement before the retrieved rainfall information generated by the GPM mission can be used effectively by prognostic models to improve weather forecasts, hydrometeorological forecasts, and climate model reanalysis simulations is a capability to quantify the error characteristics of the retrievals. A solution for this problem has been upheld in past precipitation missions because of the lack of suitable error modeling systems incorporated into the validation programs and data distribution systems. An overview of how NASA intends to overcome this problem for the GPM mission using a physically-based error modeling approach within a multi-faceted validation program is described. The solution is to first identify specific user requirements and then determine the most stringent of these requirements that embodies all essential error characterization information needed by the entire user community. In the context of NASA s scientific agenda for the GPM mission, the most stringent user requirement is found within the data assimilation community. The fundamental theory of data assimilation vis-a-vis ingesting satellite precipitation information into the pre-forecast initializations is based on quantifying the conditional bias and precision errors of individual rain retrievals, and the space-time structure of the precision error (i.e., the spatial-temporal error covariance). By generating the hardware and software capability to produce this information in a near real-time fashion, and to couple the derived quantitative error properties to the actual retrieved rainrates, all key validation users can be satisfied. The talk will describe the essential components of the hardware and software systems needed to generate such near real-time error properties, as well as the various paradigm shifts needed within the validation community to produce a validation program relevant to the precipitation user community.

Smith, Eric A.↗

Hurricane Forecasts with a Global Mesoscale-resolving Model on the NASA Columbia Supercomputer Preliminary Simulations of Hurricane Katrina (2005)

It is known that the General Circulation Models (GCMs) have sufficient resolution to accurately simulate hurricane near-eye structure and intensity. To overcome this limitation, the mesoscale-resolving finite-element GCM (fvGCM) has been experimentally deployed on the NASA Columbia supercomputer, and its performance is evaluated choosing hurricane Katrina as an example in this study. On late August 2005 Katrina underwent two stages of rapid intensification and became the sixth most intense hurricane in the Atlantic. Six 5-day simulations of Katrina at both 0.25 deg and 0.125 deg show comparable track forecasts, but the 0,125 deg runs provide much better intensity forecasts, producing center pressure with errors of only +/- 12 hPa. The 0.125 deg simulates better near-eye wind distributions and a more realistic average intensification rate. A convection parameterization (CP) is one of the major limitations in a GCM, the 0.125 deg run with CP disabled produces very encouraging results.

Shen, B.-W.↗

Deconvoluting the Friction Stir Weld Process for Optimizing Welds

In the friction stir welding process, the rotating surfaces of the pin and shoulder contact the weld metal and force a rotational flow within the weld metal. Heat, generated by the metal deformation as well as frictional slippage with the contact surface, softens the metal and makes it easier to deform. As in any thermo-mechanical processing of metal, the flow conditions are critical to the quality of the weld. For example, extrusion of metal from under the shoulder of an excessively hot weld may relax local pressure and result in wormhole defects. The trace of the weld joint in the wake of the weld may vary geometrically depending upon the flow streamlines around the tool with some geometry more vulnerable to loss of strength from joint contamination than others. The material flow path around the tool cannot be seen in real time during the weld. By using analytical "tools" based upon the principles of mathematics and physics, a weld model can be created to compute features that can be observed. By comparing the computed observations with actual data, the weld model can be validated or adjusted to get better agreement. Inputs to the model to predict weld structures and properties include: hot working properties ofthe metal, pin tool geometry, travel rate, rotation and plunge force. Since metals record their prior hot working history, the hot working conditions imparted during FSW can be quantified by interpreting the final microstructure. Variations in texture and grain size result from variations in the strain accommodated at a given strain rate and temperature. Microstructural data from a variety of FSWs has been correlated with prior marker studies to contribute to our understanding of the FSW process. Once this stage is reached, the weld modeling process can save significant development costs by reducing costly trial-and-error approaches to obtaining quality welds.

Schneider, Judy↗

Estimating Software Reliability for Space Launch Vehicles in Probabilistic Risk Assessment (PRA)

It is acutely recognized in the Probabilistic Risk Assessment (PRA) field that software plays a defining role in overall system reliability for all modern systems across a wide variety of industries. Regardless of whether the software is embedded firmware for working components or elements, part of a Human-Machine-Interface, or automated command and control logic, the success of the software to fulfill its function under nominal and off-nominal environments will be a dominant contributor to system reliability. It is also recognized that software reliability prediction and estimation is one of the more challenging and questionable aspects of any PRA or system analyses due to the nature of software and its integration with physics based systems. Irrespective of this dichotomy, any incorporation of software reliability methods requires that the contributions are accountable, quantitative, and tractable. This paper provides a brief overview of software reliability methods, establishes some minimum requirements that the methods should incorporate for completeness, and provides a logic structure for applying software reliability. Model resolution will be discussed that supports current testing plans and trade studies. We will provide initial recommendations for use in the National Aeronautics and Space Administration (NASA) PRA and present a future dynamic option for software and PRA. Space Launch Vehicle software is recognized to be reliable in static conditions, yet relatively vulnerable to a set of failure modes in changing environments/flight phases. Two quantitative methods were chosen to incorporate software reliability into a Space Launch Vehicle PRA accounting for phase adjustments. One method predicts latent software failure using statistical methods, and the second provides estimates of coding errors and software operating system failures based on test and historical data. Software uncertainty will also be discussed. It is determined that recommendations for PRA software reliability should be modeled at the software module level where multiple software components compose a module and combinations of the software architecture can lead to a functional failure.

Steven D. Novack↗

The GGCMI Phase 2 emulators: global gridded crop model responses to changes in CO2, temperature, water, and nitrogen (version 1.0)

Statistical emulation allows combining advantageous features of statistical and process-based crop models for understanding the effects of future climate changes on crop yields. We describe here the development of emulators for nine process-based crop models and five crops using output from the Global Gridded Model Intercomparison Project (GGCMI) Phase 2. The GGCMI Phase 2 experiment is designed with the explicit goal of producing a structured training dataset for emulator development that samples across four dimensions relevant to crop yields: atmospheric carbon dioxide (CO2) concentrations, temperature, water supply, and nitrogen inputs (CTWN). Simulations are run under two different adaptation assumptions: that growing seasons shorten in warmer climates, and that cultivar choice allows growing seasons to remain fixed. The dataset allows emulating the climatological-mean yield response of all models with a simple polynomial in mean growing-season values. Climatological-mean yields are a central metric in climate change impact analysis; we show here that they can be captured without relying on interannual variations. In general, emulation errors are negligible relative to differences across crop models or even across climate model scenarios; errors become significant only in some marginal lands where crops are not currently grown. We demonstrate that the resulting GGCMI emulators can reproduce yields under realistic future climate simulations, even though the GGCMI Phase 2 dataset is constructed with uniform CTWN offsets, suggesting that the effects of changes in temperature and precipitation distributions are small relative to those of changing means. The resulting emulators therefore capture relevant crop model responses in a lightweight, computationally tractable form, providing a tool that can facilitate model comparison, diagnosis of interacting factors affecting yields, and integrated assessment of climate impacts.

James A Franke↗

EXPRES. II. Searching for Planets around Active Stars: A Case Study of HD 101501

By controlling instrumental errors to below 10 cm s{sup −1}, the EXtreme PREcision Spectrograph (EXPRES) allows for a more insightful study of photospheric velocities that can mask weak Keplerian signals. Gaussian processes (GP) have become a standard tool for modeling correlated noise in radial velocity data sets. While GPs are constrained and motivated by physical properties of the star, in some cases they are still flexible enough to absorb unresolved Keplerian signals. We apply GP regression to EXPRES radial velocity measurements of the 3.5 Gyr old chromospherically active Sun-like star, HD 101501. We obtain tight constraints on the stellar rotation period and the evolution of spot distributions using 28 seasons of ground-based photometry, as well as recent Transiting Exoplanet Survey Satellite data. Light-curve inversion was carried out on both photometry data sets to reveal the spot distribution and spot evolution timescales on the star. We find that the >5 m s{sup −1} rms radial velocity variations in HD 101501 are well modeled with a GP stellar activity model without planets, yielding a residual rms scatter of 45 cm s{sup −1}. We carry out simulations, injecting and recovering signals with the GP framework, to demonstrate that high-cadence observations are required to use GPs most efficiently to detect low-mass planets around active stars like HD 101501. Sparse sampling prevents GPs from learning the correlated noise structure and can allow it to absorb prospective Keplerian signals. We quantify the moderate to high-cadence monitoring that provides the necessary information to disentangle photospheric features using GPs and to detect planets around active stars.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Maximizing energy efficiency in wastewater treatment plants: A data-driven approach for waste heat recovery and an economic analysis using Organic Rankine Cycle and thermal energy storage

Maximizing energy efficiency through waste heat recovery (WHR) processes is crucial for sustainable and ecofriendly operations across multiple industries, notably in wastewater treatment plants (WWTPs). This work proposes a comprehensive approach for assessing the WHR feasibility in WWTPs, structured in two main objectives. Firstly, an Artificial Neural Network (ANN) model is developed to accurately predict WHR based on operational data, including biogas temperature, biogas pressure, daily production in kWh, and WHR values in kWh th . The second objective focuses on economically evaluating the WHR feasibility based on the estimated WHR values obtained by the ANN model, and then realistically assessing the economic feasibility of integrating the Organic Rankine Cycle (ORC) and Seasonal Thermal Energy Storage (STES) systems. With an application to the As-Samra WWTP located in Jordan, the developed ANN model demonstrates promising results in the validation phase, with a root mean square error (RMSE) of 2206 kWh/day, a mean absolute error (MAE) of 1674 kWh/day, and an R-squared (R 2 ) value of 68%. On the other hand, the economic analysis reveals that an optimal ORC system of 412.14 kW e capacity yields a Net Present Value (NPV) of 2.09 million US dollars, a Levelized Cost of Energy (LCOE) of 0.0749 USD/kWh, a Payback Period (PBP) of 4.8 years, and annual revenues of 428 kUSD. This work also investigates the techno-economic feasibility of integrating ORC-STES. Results indicate that the LCOE and PBP are highly affected by the ORC's capital cost, and integrating STES increases the LCOE to 0.0824 USD/kWh, rendering its integration with ORC infeasible. In conclusion, this study aims to advance the understanding and application of WHR in WWTPs, paving the way for more efficient and sustainable practices in the field.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Three dimensional cluster analysis for atom probe tomography using Ripley’s K-function and machine learning

The size and structure of spatial molecular and atomic clustering can significantly impact material properties and is therefore important to accurately quantify. Ripley’s K-function (K(r)), a measure of spatial correlation, can be used to perform such quantification when the material system of interest can be represented as a marked point pattern. This work demonstrates how machine learning models based on K (r)-derived metrics can accurately estimate cluster size and intra-cluster density in simulated three dimensional (3D) point patterns containing spherical clusters of varying size; over 90% of model estimates for cluster size and intra-cluster density fall within 11% and 18% error of the true values, respectively. These K (r)-based size and density estimates are then applied to an experimental APT reconstruction to characterize MgZn clusters in a 7000 series aluminum alloy. Here we find that the estimates are more accurate, consistent, and robust to user interaction than estimates from the popular maximum separation algorithm. Using K (r) and machine learning to measure clustering is an accurate and repeatable way to quantify this important material attribute.

36 MATERIALS SCIENCE↗

Autonomous reinforcement learning agent for chemical vapor deposition synthesis of quantum materials

Abstract Predictive materials synthesis is the primary bottleneck in realizing functional and quantum materials. Strategies for synthesis of promising materials are currently identified by time-consuming trial and error and there are no known predictive schemes to design synthesis parameters for materials. We use offline reinforcement learning (RL) to predict optimal synthesis schedules, i.e., a time-sequence of reaction conditions like temperatures and concentrations, for the synthesis of semiconducting monolayer MoS 2 using chemical vapor deposition. The RL agent, trained on 10,000 computational synthesis simulations, learned threshold temperatures and chemical potentials for onset of chemical reactions and predicted previously unknown synthesis schedules that produce well-sulfidized crystalline, phase-pure MoS 2 . The model can be extended to multi-task objectives such as predicting profiles for synthesis of complex structures including multi-phase heterostructures and can predict long-time behavior of reacting systems, far beyond the domain of molecular dynamics simulations, making these predictions directly relevant to experimental synthesis.

36 MATERIALS SCIENCE↗

Gate-free state preparation for fast variational quantum eigensolver simulations

Abstract The variational quantum eigensolver is currently the flagship algorithm for solving electronic structure problems on near-term quantum computers. The algorithm involves implementing a sequence of parameterized gates on quantum hardware to generate a target quantum state, and then measuring the molecular energy. Due to finite coherence times and gate errors, the number of gates that can be implemented remains limited. In this work, we propose an alternative algorithm where device-level pulse shapes are variationally optimized for the state preparation rather than using an abstract-level quantum circuit. In doing so, the coherence time required for the state preparation is drastically reduced. We numerically demonstrate this by directly optimizing pulse shapes which accurately model the dissociation of H 2 and HeH + , and we compute the ground state energy for LiH with four transmons where we see reductions in state preparation times of roughly three orders of magnitude compared to gate-based strategies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

In silico evidence for sequence-dependent nucleosome sliding

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics.

59 BASIC BIOLOGICAL SCIENCES↗

Spectral partitioning with blends of eigenvectors

We report many common methods for data analysis rely on linear algebra. We provide new results connecting data analysis error to numerical accuracy in the context of spectral graph partitioning. We provide pointwise convergence guarantees so that spectral blends (linear combinations of eigenvectors) can be employed to solve data analysis problems with confidence in their accuracy. We apply this theory to an accessible model problem, the ring of cliques, by deriving the relevant eigenpairs and finding necessary and sufficient solver tolerances. Analysis of the ring of cliques provides an upper bound on eigensolver tolerances for graph partitioning problems. These results bridge the gap between linear algebra based data analysis methods and the convergence theory of iterative approximation methods. These results explain how the combinatorial structure of a problem can be recovered much faster than numerically accurate solutions to the associated linear algebra problem.

97 MATHEMATICS AND COMPUTING↗